Genotyping and Expression Analysis of the Non-Truncated LcELF3 Gene Shows a Link with Early Flowering in Lentil (Lens culinaris Medik.)

Lentil is an important legume crop that exhibits substantial variation in flowering time (FT). This trait is controlled by a complex but well-characterized regulatory system in many plant species, in which the Early Flowering 3 (ELF3) gene functions as a repressor of the Flowering Locus T (FT) gene. In the present study, two distinct genes, LcELF3a and LcELF3b, were identified in lentil. Sequencing of the LcELF3a gene confirmed the absence of the elf3 mutation in studied accessions, which causes a truncated polypeptide and a very early-flowering phenotype in lentil plants. Natural genetic variation, consisting of six SNPs and one insertion/deletion (InDel), but lacking the elf3 mutation, was grouped into two haplotypes, A and B, which were significantly associated with late and early flowering time, respectively. Genotyping using the newly developed ASQ marker LcELF3a-SNP3 revealed clear allele discrimination in both a lentil germplasm collection and hybrid breeding lines, identifying the homozygous genotypes aa and bb. The genotyping results with the LcELF3a-SNP3 marker confirmed that lentil accessions were associated with either late or early flowering time. Gene expression analysis using RT-qPCR in hybrid breeding lines and their parental genotypes showed high transcript levels of the LcELF3a and LcFTa1 genes. Expression of the LcELF3a gene gradually declined, while flowering initiation progressed concomitantly with the upregulation of LcFTa1 transcript accumulation. The expression of LcELF3b followed a similar pattern to that of LcELF3a, although at levels approximately four times lower. None of the other three LcFT genes (LcFTa2, LcFTb1/b2, and LcFTc) showed significant associations with flowering time in the hybrid breeding lines and parental genotypes examined. Seed yield was significantly higher in early FT cv.Krapinka and in late FT parent Flip92-36L, and in corresponding breeding lines, with aa and bb genotype of LcELF3a, respectively, whereas no differences were found between early- and late-flowering genotypes in the lentil germplasm collection. Other traits associated with adaptation to local environmental conditions are likely to have a greater influence on seed yield in lentil.